Following an exercise in the UK, I travelled directly to a 5 day course in Germany - both away from my duty station.
Would my LSA stop on the day I left the exercise or would it continue up to the last day of the course?

If you did not return to your duty station / home I would say that it should continue as you are still absent from both of them and unable to travel back during periods of standdown.

There used to be a rule if you got LSA, and then went back to your unit, but then went away again on LSA qualifying separation less than 10 days later then you would have it for the whole period (not sure if that is still in the regs though)